This is going to be a long one from me, so you'll have to forgive me.
The first part of it is that it's very expensive. While it's great, the cost behind it makes it a spiral. If you want some decent bioware, you need the money, you bioware has been damaged/detected and removed or a new model is what you're now after, you're going to need the nuyen to get it, meaning you're working and need some pretty good jobs or a good run of successful runs.
While the character is certainly doing his job, I would still have a look at the type of security you're having the team up against. There's something that should be able to hurt them held on stand by in every major office, team. There's got to be something that makes them pull back. Geek the mage first is said for a reason and a good place to start.
As for detection of it, I'd look to the above posts, they offer some good options. Bad luck happens to everyone, and you might be dealing with someone who really thinks the metahuman body is sacred and should not be changed, biologically or cybernetically. There are plenty of ways to detect it, if you're looking for it.
As well as that, on the security side, I think you should look at general security for where he goes too. Bioware, because it is so expensive, makes him a target of bioware harvesting groups. If he wants that type of character, he should pay the price. Especially if he's got a fair bit of work done. Each time he's goes in for a new piece, remind him that he might not actually wake up. Sure it's something of a cheap shot, but this is Shadowrun and more importantly it's also what makes sense in my mind. It's revenge and profit combined into one neat little package.
On the subject of revenge, the use of an assault cannon is encouraged here. If people know him for being said wall of flesh, then they'll take active measures to either disable or to work around.
Try and build situations up for options that don't involve extreme violence. Give the group tasks that are only offered because the troll is known as being a reflective bullet magnet. Make him do the negotiations and build on challenges in those runs that while he's needed to take hits, some pretty big ones, there's still plenty for the others to do. Play on the team identity as well, across the whole group.
Chemical, magic, also presents options and have been well listed above. Same goes elemental types of damage.
On a personal note, when it comes to the low Essence part of it, I had an idea in my mind for that. I suppose I see it as the spark, creative force, that some people have. That thing which makes them stand out, makes Mick Jagger, Mick Jagger. That if he's pursuing any sort of creative path, art, performing etc, that things feel different, harder. That things are more..... technical, less creative. That music feels duller, less intensive, inspiring, emotional. Art he loved is now that little bit boring, he needs to be in the right mood to enjoy it. Same goes for anything that the character particularly enjoys.
I'd even have gone as far as to have subtle reactions, that people don't seem to notice him at first. It's hard to explain to be honest. It's like everyone is slightly distracted when it comes to him. They need to focus a little more on the fact he is physically there. This isn't any sort of active stealth or hiding, more that there's something less notable about his troll. I wouldn't go so far as to describe this character as a meat shell, but there's something about the character that just rubs the more sensitive the wrong way. They don't need to be adepts or magicians either, there's just something less about them that makes people react badly.
Imagine going in to buy some food and the metahuman behind the counter screams at you to get out, which causes building security to come in and escort you out. That's perhaps taking it a little further than I might, but is none the less an option. Perhaps being charged a little more for basic purchases every so often, or selling things for a little less than he should get as well. That he needs to repeat himself every so often, as he's not obviously noticed. People might walk into him for being so busy, really it's from the low Essence. I'd supporting many different ideas, as long as they were subtle, gentle and creative. Like all of those little frustrations that you get over the course of a too long day.
I plan on making this apply to all characters of less than two, three essence.
